User: muraved

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muraved0
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Posts by muraved

<prev • 15 results • page 1 of 2 • next >
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Low SNP imputation concordance - except chromosome 1
... Hi, I'm trying to do SNP imputation using IMPUTE2. My genotype data (bim/bed/fam) is hg18, with the usual quality control, mostly European ancestry, reference panel is hg19. My workflow: 1. Determine flipped and ambiguous SNPs relative to hg18, using snpflip (https://github.com/biocore-ntnu/snpfl ...
impute2 imputation plink snp gwas written 29 days ago by muraved0
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Comment: C: SNP coordinates and 1KG
... Well, that's a matter of perspective ;-) If one works with older data, like myself, there's a need for that as demonstrated by this question ;-) Would be nice to get ALL available information for a given Snp. ...
written 4 weeks ago by muraved0
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Comment: C: SNP coordinates and 1KG
... Thanks. Didn't know dbSNP did not provide hg18 coordinates. ...
written 4 weeks ago by muraved0
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SNP coordinates and 1KG
... I have some genotype data which gives me some problems, and I suspect that the genome build is not what it is supposed to be. I have a bim file with the following line: 1 rs2465136 0 980280 G A According to dbSNP (https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=24 ...
gwas snp written 4 weeks ago by muraved0 • updated 4 weeks ago by finswimmer5.4k
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PRSice: Imputation and clumping
... I am trying to use PRSice. Unfortunately, my target sample has fewer SNPs than my discovery/base sample, as it comes from different platforms. My question is of a methodological nature: I could of course impute the missing SNPs, and PRSice explicitely mentions it can handle such information. However ...
prsice gwas polygenic risk score snp written 5 weeks ago by muraved0 • updated 17 days ago by Sam2.1k
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Comment: C: How exactly does MAQ handle mate-pair data
... Oops... thanks for pointing that out, I must've missed that :-/ ...
written 14 months ago by muraved0
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Answer: A: How exactly does MAQ handle mate-pair data
... Thanks. Hmm, so, there is no input specification of whether it's paired-end or mate-pair. For an input like maq map F.fq R.fq, it simpy checks the relative positions of mapping locations, and accepts F-R as specified by -a, and R-F as specified by -A then? ...
written 14 months ago by muraved0
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Comment: C: How exactly does MAQ handle mate-pair data
... As you will notice, my question has the exact same link you provided. The specifics I am asking for are not explained on the man page in my opinion. But maybe I'm overlooking something. ...
written 14 months ago by muraved0
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Comment: C: How exactly does MAQ handle mate-pair data
... Thanks for the link. I am well aware of several read mappers for MP mapping, I'm really asking specifically about MAQ. I do appreciate your help, though :-) ...
written 14 months ago by muraved0
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Comment: C: How exactly does MAQ handle mate-pair data
... Yes. The way it does consensus calling lends itself to read correction. I'm not so much interested in the alignment itself. Also, old doesn't mean bad ;-) ...
written 14 months ago by muraved0

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Popular Question 14 months ago, created a question with more than 1,000 views. For samtools depth for start positions
Popular Question 14 months ago, created a question with more than 1,000 views. For Allele intensities from SNP arrays

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